Sequence
atgc intronic sequence ATGC exonic sequence...aatttctcatataaattggcacaactttttttcttaataatattgtttgaaattatggtgttgaattttttaattgttgtttctcattctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
Basic information
species | Glycine max |
transcript | GLYMA20G35460.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G096169_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------------------------aatttctcatataaattggcacaactttttttcttaataatattgtttgaaattatggtgttgaattttttaattgttgtttctcattctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
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gtgagctgttagttcgtttccctgagatttctgcacagcatatttaccagcatgaatgggatgtcattcgtcat-tgtactgtagtgatttattagattcatcattgtatcagggtagctgagatagcaggagttgatatttgctttctga-ctgtgcagATAA-TTGTGATCTATATCGTGGAGAGTGGGTTACTGATTCTTCTGGGCCACTATACACAAACAACTCCTGCCCTATCATCACACAGATGCAGAATTGCCA---
upper sequence: GLYMA20G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25360.1 (Arabidopsis thaliana), 3'ss of exon 2
aatttctcatataaattggcacaacttttt----ttcttaataat-attgtttgaaattatggtgttgaattttttaattgttgtttctcattctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
|| | | | || | ||| | |||| | | ||||| | ||| || ||| ||| | || | || || | |||||| |||||| |||| || || | |||| | ||||||| |||||| | ||||| ||||| || |||||||| |||| ||||||||||||||||||||
----gttcttgtcagtttcccttgcttctcatgattctagctgttcgatgttttatatttctgttatgagtttgtcgcttact-caaatctttgattgcttgtagAGTGTGATTTGTATCAAGGTAGTTGGTTTTATGATCCTGGGGGACCTCTCTACACGAACAACTCTTGCCCTGTCCTGACGCAGATGCAGAATTGCCAGGG
upper sequence: GLYMA20G35460.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0022g01830.t01 (Vitis vinifera), 3'ss of exon 1
aatttctcatataaattggcacaactttttttcttaataatattgtttgaaattatggtgttgaattt----tttaattgttgtttctcatt--ctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
| | ||| | | | | | || || || |||| || | | |||| ||| | | | | || | | ||||| |||| || |||| ||||||||||||||||| | |||| | ||||| || ||||||| |||||||||||| |||||||||| |||||||||||||| |||||||||||
-----gtgttgtaagctagaaatattcattctccagattgtattacttcttgatttcttgtttcttttaagctcttaatattctgtttcattggttgttctt-tagGGTGTGATCTGTACCATGGGAGTTGGTTTTATGATTCATCTGGACCATCATACACAAACAACACATGCCCTGTTTTGACACAGATGCAAAATTGCCAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttgaaattatggtgttgaattttttaattgttgtttctcattctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
ttttaat putative branch site (score: 3)
tttctcattctgtttt putative PPT
ttgaattttttaattg TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatttctcatataaattggcacaactttttttcttaataatattgtttgaaattatggtgttgaattttttaattgttgtttctcattctgtttttgtagGCTGTGATCTGTACCATGGAAATTGGATACATGATCCACTGGGACCATTATACACAAACAATTCATGCCCTGTATTGACACAGATGCAGAATTGCCAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - gcacaac
- - - - - - - - - - - - - - - - - - - - - ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtgttg